Buck, Damian P., Spillane, Caitriona B., Collins, J. Grant, and Keene, F. Richard (2008) Binding of a dinuclear ruthenium(II) complex to the TAR region of the HIV-AIDS viral RNA. Molecular BioSystems, 4. pp. 851-854.

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Abstract

Molecular modelling has identified a new RNA conformational feature created by the insertion of bulge residues into duplex regions that may act as a recognition site for small molecule binding, in particular for inert dinuclear ruthenium complexes. We have demonstrated previously tbat inert dinuclear ruthenium(I1) complexes preferentially bind DNA and RNA at nonduplex structures, such as bulges and hairpin-loops^1-3. These features occur more frequently in RNA, and play an important role as secondary structure elements for specific recognition by proteins, RNA splicing and RNA-folding^4.5 thereby making tbem promising targets for therapeutic agents^6. Dinuclear ruthenium complexes have been shown to bind in the minor groove of RNA, which is wide but shallow, and hence does not provide a good binding site for these bulky metal complexes. However, the introduction of a non-duplex feature such as a base bulge can alter the helical structure to make a more preferable metal complex binding site.

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